{"id":"W2162193618","doi":"10.2174/1875036200802010080","title":"Modeling Cooperative Gene Regulation Using Fast Orthogonal Search","year":2008,"lang":"en","type":"article","venue":"The Open Bioinformatics Journal","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":5,"is_retracted":false,"has_abstract":true,"ca_institutions":"Queen's University","funders":"Lawrence Berkeley National Laboratory","keywords":"Motif (music); Saccharomyces cerevisiae; Computer science; Computational biology; Transcription factor; Gene; Gene regulatory network; Biology; Gene expression; Genetics","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0009244701,0.0006289119,0.0008144846,0.0006750562,0.0003961361,0.0005867204,0.001109819,0.0009950347,0.001247198],"category_scores_gemma":[0.002291327,0.0005194539,0.0008988869,0.0007675253,0.0007503412,0.0007225169,0.000812499,0.0005456072,0.0002117747],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007924435,"about_ca_system_score_gemma":0.001137285,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.01061816,"about_ca_topic_score_gemma":0.007788451,"domain_scores_codex":[0.9996902,0.0001153921,0.00001392936,0.00006156116,0.00007472701,0.00004421315],"domain_scores_gemma":[0.9989744,0.0007563942,0.00008697874,0.0000580313,0.00008457204,0.00003968252],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.00002318085,0.00001358522,0.0003041411,0.000008032691,0.00001005262,0.00001669609,0.00001148643,0.9928483,0.0006629484,0.003585075,0.00005626211,0.002460332],"study_design_scores_gemma":[0.000003354463,0.000003612657,0.00001480582,2.603699e-7,9.466308e-7,0.000001866166,0.000001193421,0.9989582,0.00008152239,0.0008928653,0.00004033419,8.957668e-7],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.1878809,0.0002119246,0.8072388,0.0001754061,0.00002306662,0.00005571819,0.0001620913,0.0007126672,0.003539424],"genre_scores_gemma":[0.8246543,0.0002280625,0.1707173,0.0000768808,0.00002062251,0.0003403767,0.0002445451,0.0001495562,0.003568312],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.01061816,"threshold_uncertainty_score":0.02111268,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04184068761405676,"score_gpt":0.2821583290921968,"score_spread":0.2403176414781401,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}